RHOBTB2 Variant p.Arg511Gln Causes Developmental and Epileptic Encephalopathy Type 64 in an Infant: A Case Report and Hotspot Variant Analysis by Qian Liu, Feifei Li, Qin Ruan, Nana Wang, Zhengjun Fan

“…We used Discovery Studio software to analyze the folding free energy of variant proteins, and the AlphaFold database to analyze structural alterations in mutant proteins. …”
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Non-Steroidal Anti-Inflammatory Drugs Are Inhibitors of the Intestinal Proton-Coupled Amino Acid Transporter (PAT1): Ibuprofen and Diclofenac Are Non-Translocated Inhibitors by Carsten Uhd Nielsen, Sebastian Jakobsen, Maria L. Pedersen

“…The molecular interaction between NSAIDs and hPAT1 was investigated using an AlphaFold2 model and molecular docking. <b>Results:</b> NSAIDs such as ibuprofen, diclofenac, and flurbiprofen inhibited proline uptake via hPAT1, with IC₅₀ values of 954 (logIC₅₀ 2.98 ± 0.1) µM, 272 (logIC₅₀ 2.43 ± 0.1) µM, and 280 (logIC₅₀ 2.45 ± 0.1) µM, respectively. …”
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Computational biology assisted exploration of phytochemicals derived natural inhibitors to block BZLF1 gene activation of Epstein–Bar virus in host by Muhammad Naveed, Muzamal Hussain, Tariq Aziz, Nimra Hanif, Nazia Kanwal, Arooj Arshad, Ayaz Ali Khan, Abdulrahman Alshammari, Metab Alharbi

“…Various bioinformatics methods were employed to predict and analyze the toxin protein structure obtained from NCBI, and its secondary and tertiary structures were predicted using PSIPRED and the AlphaFold. ProtParam was used to assess physiochemical characteristics. …”
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Biochemical and structural characterization of Rab3GAP reveals insights into Rab18 nucleotide exchange activity by Gage M. J. Fairlie, Kha M. Nguyen, Sung-Eun Nam, Alexandria L. Shaw, Matthew A. H. Parson, Hannah R. Shariati, Xinyin Wang, Meredith L. Jenkins, Michael Gong, John E. Burke, Calvin K. Yip

“…Our high-resolution structure of the catalytic core of Rab3GAP, determined by cryo-EM, shows that the Rab3GAP2 N-terminal domain binds Rab3GAP1 via an extensive interface. AlphaFold3 modelling analysis together with targeted mutagenesis and in vitro activity assay reveal that Rab3GAP likely engages its substrate Rab18 through an interface away from the switch and interswitch regions. …”
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Identification and characterization of the functional tetrameric UDP-glucose pyrophosphorylase from Klebsiella pneumoniae by Isabel Ramón Roth, Pavel Kats, Timm Fiebig, Françoise Routier, Roman Fedorov, Larissa Dirr, Jana I. Führing

“…Here, we show that the galF gene of the opportunistic pathogen Klebsiella pneumoniae encodes a dimeric protein that has lost UGP activity, likely due to a combination of active site mutations and an inability to tetramerize, whereas the functional K. pneumoniae UGP, encoded by galU, is an active tetramer. Our AlphaFold-assisted structure-function relationship studies underline that tetramerization is essential for bacterial UGP function and is facilitated by a common mechanism utilizing conserved key residues. …”
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S‐PLM: Structure‐Aware Protein Language Model via Contrastive Learning Between Sequence and Structure by Duolin Wang, Mahdi Pourmirzaei, Usman L. Abbas, Shuai Zeng, Negin Manshour, Farzaneh Esmaili, Biplab Poudel, Yuexu Jiang, Qing Shao, Jin Chen, Dong Xu

“…S‐PLM applies Swin‐Transformer on AlphaFold‐predicted protein structures to embed the structural information and fuses it into sequence‐based embedding from ESM2. …”
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Bioinformatics and Expression Profiling of the DHHC-CRD S-Acyltransferases Reveal Their Roles in Growth and Stress Response in Woodland Strawberry (<i>Fragaria vesca</i>) by Si Gu, Xinghua Nie, Amal George, Kyle Tyler, Yu Xing, Ling Qin, Baoxiu Qi

“…A complementation assay in yeast PAT mutant <i>akr1</i> and auto-S-acylation assay of one FvPAT (FvPAT19) confirmed its enzyme activity where the Cys in the DHHC motif was required. An AlphaFold prediction of the DHHC and the mutated DHHC155S of FvPAT19 provided further proof of the importance of C155 in fatty acid binding. …”
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Genome-Wide Study of Plant-Specific PLATZ Transcription Factors and Functional Analysis of <i>OsPLATZ1</i> in Regulating Caryopsis Development of Rice (<i>Oryza sativa</i> L.) by Tao Yang, Xin-Tong Xu, Li-Jun Tang, Wen-Tao Wei, Yuan-Yuan Zhao, Jin-Xin Liu, Xue-Feng Yao, Heng Zhao, Chun-Ming Liu, Ai-Ning Bai

“…Most of the OsPLATZs localized to the nuclei, and were predicted to bind to DNA sequences by AlphaFold3, suggesting that they likely function as conventional transcription factors. …”
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Deep learning–based assessment of missense variants in the COG4 gene presented with bilateral congenital cataract by Shaohua Zhang, Yang Sun, Yinghong Ji, Li Ning, Binghe Xiao, Maierdanjiang Ainiwaer, Houyi Liu, Yingying Hong

“…Objective We compared the protein structure and pathogenicity of clinically relevant variants of the COG4 gene with AlphaFold2 (AF2), Alpha Missense (AM), and ThermoMPNN for the first time.Methods and analysis The sequences of clinically relevant Cog4 missense variants (one novel identified p.Y714F and three pre-existing p.G512R, p.R729W and p.L769R from Uniprot Q9H9E3) were imported into AF2 for protein structural prediction, and the pathogenicity was estimated using AM and ThermoMPNN. …”
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Mapping knowledge landscapes and emerging trends in artificial intelligence for antimicrobial resistance: bibliometric and visualization analysis by Zhongli Wang, Zhongli Wang, Gaopei Zhu, Shixue Li, Shixue Li

“…Citation analysis highlighted two major breakthroughs: AlphaFold’s protein structure prediction (6,811 citations) and deep learning approaches to antibiotic discovery (4,784 citations). …”
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Acetylation of proximal cysteine-lysine pairs by alcohol metabolism by Courtney D. McGinnis, Peter S. Harris, Brenton I.M. Graham, John O. Marentette, Cole R. Michel, Laura M. Saba, Richard Reisdorph, James R. Roede, Kristofer S. Fritz

“…Interrogating both cysteine redox and lysine acetylation datasets, 1280 protein structures generated by AlphaFold2 represented by a 3D spatial matrix were used to quantify the distances between 557,815 cysteine and lysine residues. …”
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The protein structurome of Orthornavirae and its dark matter by Pascal Mutz, Antonio Pedro Camargo, Harutyun Sahakyan, Uri Neri, Anamarija Butkovic, Yuri I. Wolf, Mart Krupovic, Valerian V. Dolja, Eugene V. Koonin

“…The rest of the viral proteome seems to be dominated by poorly structured domains including intrinsically disordered ones that likely mediate specific virus-host interactions.IMPORTANCEAdvanced methods for protein structure prediction, such as AlphaFold2, greatly expand our capability to identify protein domains and infer their likely functions and evolutionary relationships. …”
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Tat-fimbriae (“tafi”): An unusual type of haloarchaeal surface structure depending on the twin-arginine translocation pathway by Anna V. Galeva, Dahe Zhao, Alexey S. Syutkin, Marina Yu Topilina, Sergei Yu Shchyogolev, Elena Yu Pavlova, Olga M. Selivanova, Igor I. Kireev, Alexey K. Surin, Gennady L. Burygin, Jingfang Liu, Hua Xiang, Mikhail G. Pyatibratov

“…Based on protein structure prediction (including AlphaFold 3), tafi exhibits a linear structure: TafC at the tip, TafE acting as an adapter, TafA forming the core filament, and they link the fourth subunit TafF, anchoring tafi to the cell wall. …”
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A rare haplotype of the GJD3 gene segregating in familial Meniere’s disease interferes with connexin assembly by Alba Escalera-Balsera, Paula Robles-Bolivar, Alberto M. Parra-Perez, Silvia Murillo-Cuesta, Han Chow Chua, Lourdes Rodríguez-de la Rosa, Julio Contreras, Ewa Domarecka, Juan Carlos Amor-Dorado, Andrés Soto-Varela, Isabel Varela-Nieto, Agnieszka J. Szczepek, Alvaro Gallego-Martinez, Jose A. Lopez-Escamez

“…The connexin monomer and the homomeric connexon structural models were predicted using AlphaFold2 and HDOCK. RT-qPCR and immunofluorescence were done in mice cochleae to identify expression of the mouse ortholog candidate gene Gjd3. …”
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A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases by Tesson, Florian, Planel, Rémi, Egorov, Artyom A, Georjon, Héloïse, Vaysset, Hugo, Brancotte, Bryan, Néron, Bertrand, Mordret, Ernest, Atkinson, Gemma Catherine, Bernheim, Aude, Cury, Jean

“…To overcome these challenges, we present a hub of resources on defense systems, including: 1) an updated version of DefenseFinder with a web-service search function, 2) a community-curated repository of knowledge on the systems, and 3) precomputed databases, which include annotations done on RefSeq genomes and structure predictions generated by AlphaFold. These pages can be freely accessed for users as a starting point on their journey to better understand a given system. …”
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Deciphering the role of metal ion transport-related genes in T2D pathogenesis and immune cell infiltration via scRNA-seq and machine learning by Zuhui Pu, Zuhui Pu, Tony Bowei Wang, Ying Lu, Ying Lu, Zijing Wu, Zijing Wu, Yuxian Chen, Ziqi Luo, Xinyu Wang, Lisha Mou, Lisha Mou

“…Twelve protein structures were predicted using AlphaFold 3, revealing potential functional conformations. …”
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Complexes of vertebrate TMC1/2 and CIB2/3 proteins form hair-cell mechanotransduction cation channels by Arnaud PJ Giese, Wei-Hsiang Weng, Katie S Kindt, Hui Ho Vanessa Chang, Jonathan S Montgomery, Evan M Ratzan, Alisha J Beirl, Roberto Aponte Rivera, Jeffrey M Lotthammer, Sanket Walujkar, Mark P Foster, Omid A Zobeiri, Jeffrey R Holt, Saima Riazuddin, Kathleen E Cullen, Marcos Sotomayor, Zubair M Ahmed

“…Here, we show that both CIB2 and CIB3 can form heteromeric complexes with TMC1 and TMC2 and are integral for MET function in mouse cochlea and vestibular end organs as well as in zebrafish inner ear and lateral line. Our AlphaFold 2 models suggest that vertebrate CIB proteins can simultaneously interact with at least two cytoplasmic domains of TMC1 and TMC2 as validated using nuclear magnetic resonance spectroscopy of TMC1 fragments interacting with CIB2 and CIB3. …”
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